ArticleScientific reports2022
Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 80 citations in OpenAlex.
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.BMC infectious diseases · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- Enhancing low-level genome-edited crop detection and identification in food mixtures using nanopore adaptive sampling: Rice-Soybean mixture as proof-of-concept.NPJ science of food · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Effects of aquaculture practices onApplied and environmental microbiology · 2026Article
- Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.Nucleic acids research · 2026Review
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.The New phytologist · 2025Article
- Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.Microbiome · 2025Article
- Association Between Vaginal Community States and Preeclampsia Status in Pregnant Individuals.bioRxiv : the preprint server for biology · 2025Article
- A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.Genome biology · 2025Article
- Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.Microbial genomics · 2025Article
- Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.BMC microbiology · 2025Article
- Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
- Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosis.Frontiers in microbiology · 2025Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (> 90%), decreasing the overall microbial resolution. Nanopore's adaptive sampling method offers selective DNA depletion or target enrichment to directly reject or accept DNA molecules during sequencing without specialized sample preparation. Here, we demonstrate how selective 'human host depletion' resulted in a 1.70 fold (± 0.27 fold) increase in total sequencing depth, providing higher taxonomic profiling sensitivity. At the same time, the microbial composition remains consistent with the control experiments. The complete removal of all human host sequences is not yet possible and should be considered as an ethical approval statement might still be necessary. Adaptive sampling increased microbial sequencing yield in all 15 sequenced clinical routine vaginal samples, making it a valuable tool for clinical surveillance and medical-based research, which can be used in addition to other host depletion methods before sequencing.
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